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Table 2 Sequencing metrics of AMR genes using the 1mL and 5mL CMg pipelines

From: Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection

pEK499 genes

Average Coverage (X)

Average template identity (%) /

Average Template Coverage (%)

 

1 mL protocol

5 mL protocol

1 mL protocol

5 mL protocol

50–100 CFU/mL

5–10 CFU/mL

1–5 CFU/mL

50–100 CFU/mL

5–10

CFU/mL

1–5

CFU/mL

50–100 CFU/mL

5–10

CFU/mL

1–5

CFU/mL

50–100 CFU/mL

5–10 CFU/mL

1–5 CFU/mL

blaCTX-M-15

4.1 ± 0.7

1.0 ± 1.0

0

48.9 ± 10.1

11.3 ± 1.8

17.3 ± 7.5

100.0 ± 0

/

100.0 ± 0

100.0 ± 0 /

100.3 ± 0

-

99.0 ± 0.0 /

100.0 ± 0

100.0 ± 0

/

100.0 ± 0

99.0 ± 0.1 /

100.8 ± 0.8

blaOXA-1

0

0

0

6.4 ± 1.4

2.0 ± 1.0

5.5 ± 2.8

-

-

-

100.0 ± 0

/

100.0 ± 0

99.9 ± 0.1 /

100.0 ± 0

100.0 ± 0

/

100.8 ± 0.8

blaTEM-1

1.0 ± 0.1

0

0

2.7 ± 0.1

0.7 ± 0.7

0

98.8 ± 0.3 /

100.5 ± 0.1

-

-

99.7 ± 0

/ 101.7 ± 1.2

99.4 ± 0.0 /

101.4 ± 1.4

-

aac6’-lb-cr

0

0

0

3.9 ± 2.9

1.7 ± 0.9

1.9 ± 1.1

-

-

-

99.8 ± 0.0 / 100.3 ± 0.3

98.9 ± 1.1 /

100.3 ± 0.3

99.7 ± 0.1 /

100.5 ± 0.5

mph(A)

5.6 ± 2.6

1.0 ± 0.6

0

39.8 ± 6.5

6.9 ± 1.5

13.0 ± 7.7

99.4 ± 0.6 /

100.0 ± 0

100.0 ± 0 /

100.3 ± 0

-

100.0 ± 0

/

100.0 ± 0

100.0 ± 0

/

100.0 ± 0

100.0 ± 0

/

100.0 ± 0

catB4

0

 

0

7.3 ± 1.7

1.4 ± 0.2

0.7 ± 0.7

-

-

-

92.5 ± 1.2 /

102.1 ± 0.7

86.9 ± 1.0 /

101.7 ± 1.0

94.5 ± 0

/

99.8 ± 0

tet(A)

2.3 ± 2.3

0

0

0.3 ± 0.3

0

0.3 ± 0.3

92.5 ± 0

/

101.7 ± 0

-

-

98.3 ± 0.0 /

100.2 ± 0

-

73.2 ± 0

/

77.4 ± 0

dfrA7

4.5 ± 1.5

0

0

16.5 ± 2.6

5.7 ± 0.3

3.5 ± 1.9

99.1 ± 0.8 /

100.1 ± 0.1

-

-

99.8 ± 0.0 /

100.0 ± 0

99.8 ± 0.0 /

100.0 ± 0

99.3 ± 0.5 /

100.1 ± 0.1

sulI

3.6 ± 2.0

0

0

18.7 ± 5.8

3.6 ± 1.6

3.6 ± 2.0

99.8 ± 0.2 /

100.1 ± 0.1

-

-

100.0 ± 0

/

100.1 ± 0

98.9 ± 1.2 /

100.0 ± 0

99.9 ± 0.1 /

100.1 ± 0.1

aadA5

4.9 ± 0.1

0

0

19.6 ± 3.8

9.1 ± 0.5

4.4 ± 2.6

99.0 ± 0.1 /

100.0 ± 0

-

-

99.9 ± 0.1 /

100.0 ± 0

100. ± 0.0 /

100.0 ± 0

100. ± 0

/

100.0 ± 0

  1. 1mL or 5mL of blood were spiked with E. coli CTX-M-15 (peK499 plasmid) at different concentrations (50–100, 10–50 and 1–5 CFU/mL) and subjected to ‘1mL standard protocol’ and ‘5mL quick-enrichment protocol’. AMR determinants were detected and samples were compared by assessing their coverage and template identity to the reference. Average Coverage (X) = average depth of coverage of the template. Average template identity (%) = percentage of identical nucleotides between template and consensus. Average template coverage (%) = percentage of bases in the template that is covered by consensus sequence. Data are means ± SD. n = 3 are biological replicates
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BMC Medical Genomics

ISSN: 1755-8794

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